DNA is frequently damaged by exogenous influences such as radiation, and endogenous effects such as replication stress. Repair of this damage may lead to chromosomal structural changes that change the number of copies of genes in the cells. Copy number variation is the basis of a series of inherited diseases known as genomic disorders and underlies the initiation, progression and resistance mechanisms of many cancers. Although great progress has been made in describing the detailed structures associated with copy number changes, and we have specific ideas on what mechanisms might generate the changes, we are unable to ascribe specific mechanisms to specific events. Study of the mechanisms of chromosomal change in model organisms has revealed that the repair DNA synthesis and single-strandedness associated with various mechanisms of chromosomal change is of very low fidelity, generating many point mutations. Because the pattern of repair synthesis and single-strandedness is different for different mechanisms of change, we expect that each mechanism will leave a characteristic signature in the DNA in the form of distribution and spectrum of new point mutations. Using a large collection of clinical isolates of germline and constitutive copy number variants, we plan to map these signatures to the regions of chromosomal change for different classes of copy number change to reveal the pattern of associated repair synthesis and hence the mechanism underlying specific events. Preliminary data show that the amount of new point mutation to be expected is well within the limits of detection and readily differentiated from that in chromosomal regions that are not involved in rearrangements.